This chapter discusses the roles of RecA and other proteins in homologous recombination. It also focuses on RecA's other roles, as these also contribute to increases in genetic diversity. It discusses how homologous recombination occurs at the molecular level and how this can lead to an increase in genetic diversity. It summarizes the current understanding of recA's crucial and essential role in homologous recombination, its other roles in the regulation of damage-inducible DNA-repair pathways, and its participation in mutagenic events that can lead to increases in genetic diversity. It is most convenient to think of recombination as a three-stage process. The three stages are called presynapsis, synapsis, and postsynapsis. These stages are used to discuss the processing of the DNA substrates and the enzymes that act on them. Presynapsis describes the tailoring of the DNA substrates so that they can interact with the RecA protein. If the recombination enzymes and substrates are present, the enzymes will recombine any DNA that is available with great accuracy, precision, and efficiency. The prevailing thought in the chapter is that once recombination substrates are presented to a cell, given that the cell has the proper enzymes, recombination will occur. RecA aids in the repair of double-strand breaks in DNA.

Two different types of DNA substrates that could be formed as a result of a replication fork running into a nick (formation of a double-strand end) or a noncoding lesion (square on the DNA) to form a gap. The gene products and the particular stage of recombination at which they are predicted to function are indicated.

10.1128/9781555817749/fig2-1_thmb.gif

10.1128/9781555817749/fig2-1.gif

FIGURE 1

Two different types of DNA substrates that could be formed as a result of a replication fork running into a nick (formation of a double-strand end) or a noncoding lesion (square on the DNA) to form a gap. The gene products and the particular stage of recombination at which they are predicted to function are indicated.

A three-stranded reaction, (a) RecA initially binds the ssDNA, creating a protein DNA helical filament, (b) A duplex of DNA then interacts in the major groove of the filament, (c) One strand is then exchanged for the other, (d and e) Completion of the reaction. (This figure is reprinted from Nelson and Cox [2000] with permission of the authors.)

10.1128/9781555817749/fig2-2_thmb.gif

10.1128/9781555817749/fig2-2.gif

FIGURE 2

A three-stranded reaction, (a) RecA initially binds the ssDNA, creating a protein DNA helical filament, (b) A duplex of DNA then interacts in the major groove of the filament, (c) One strand is then exchanged for the other, (d and e) Completion of the reaction. (This figure is reprinted from Nelson and Cox [2000] with permission of the authors.)

Model of a filament of RecA at the molecular level. Twenty-four monomers of the RecA crystal structure have been assembled in a filament. One monomer is shown in darker shading. (This figure is reprinted from Nelson and Cox [2000] with permission of the authors.)

10.1128/9781555817749/fig2-3_thmb.gif

10.1128/9781555817749/fig2-3.gif

FIGURE 3

Model of a filament of RecA at the molecular level. Twenty-four monomers of the RecA crystal structure have been assembled in a filament. One monomer is shown in darker shading. (This figure is reprinted from Nelson and Cox [2000] with permission of the authors.)

Formation of a Holliday junction, its isomerization between the crossover and open-planar forms, and its resolution into patched and crossover recombinants. The arrows pointing to the strands in the Holliday junction are indicative of the strands cleaved by RuvC. Note that pairs of strands are cleaved to form the recombinants. The letters provide orientation for how the arms of the structure are rotated in space. The double arrows indicate isomerization.

10.1128/9781555817749/fig2-4_thmb.gif

10.1128/9781555817749/fig2-4.gif

FIGURE 4

Formation of a Holliday junction, its isomerization between the crossover and open-planar forms, and its resolution into patched and crossover recombinants. The arrows pointing to the strands in the Holliday junction are indicative of the strands cleaved by RuvC. Note that pairs of strands are cleaved to form the recombinants. The letters provide orientation for how the arms of the structure are rotated in space. The double arrows indicate isomerization.

Replication fork reversal. The two differently shaded strands indicate parental and newly synthesized DNA. The enzymes that are known to catalyze this reaction are shown at the sides. Although only RecG is mentioned in the text as an enzyme that can perform this reaction, there is evidence that RuvAB also catalyzes this reaction. The letters provide orientation for how the arms of the structure are rotated in space. The double arrows indicate isomerization.

10.1128/9781555817749/fig2-5_thmb.gif

10.1128/9781555817749/fig2-5.gif

FIGURE 5

Replication fork reversal. The two differently shaded strands indicate parental and newly synthesized DNA. The enzymes that are known to catalyze this reaction are shown at the sides. Although only RecG is mentioned in the text as an enzyme that can perform this reaction, there is evidence that RuvAB also catalyzes this reaction. The letters provide orientation for how the arms of the structure are rotated in space. The double arrows indicate isomerization.